I am analyzing my RNA-seq data on Galaxy platform using Tophat-Cufflink-Cuffdiff pipeline. I aligned my reads with hg38 but for cuffdiff I need a well annotated, working hg38 gtf file. I already tried a gtf file on hg38 from UCSC but it didn't work.
Is there someone done such analysis on hg38 gtf file? If so, please provide me the download link for the same.